Hmm, the bug report
https://bugs.launchpad.net/calibre/+bug/1523291 suggested removing the Kobo Utilities plug-in, but still got the same issue after doing that. I'm seeing the switched main/SD card card (2Gb/8Gb) issue, get errors when ejecting the device from Calibre or the Mac (eject card first and eject Kobo first), and Calibre takes a while to get the book list from the Kobo. When I transfer books, I usually have to try multiple times to get all books across.
I cannot find the original thread here on MR.
I'm only running the standard Kobo plug-in not the extended, and Calibre, Kobo firmware and Mac OS are all up-to-date. So I don't know what to try next...